Data files to integrate

All data required to build an InterMine is included in bio/tutorial/malariamine/malaria-data.tar.gz. Copy this file to your local directory and extract from the archive.

cp bio/tutorial/malariamine/malaria-data.tar.gz DATA_DIR
cd DATA_DIR
tar -zxvf malaria-data.tar.gz

Edit the project.xml file so that all occurances of DATA_DIR point to the your local data directory location.

Data sources

malaria-genome

The malaria genome as gff3 and fasta, originally downloaded from PlasmoDB

uniprot

UniProt XML with protein information and sequences from SwissProt and Trembl. Downloaded from: http://www.ebi.ac.uk/uniprot/database/download.html and filtered on taxon id 36329.

gene_ontology

The Gene Ontology structure. Downloaded from http://www.geneontology.org/

go_annotation

GO term assignments for P. falciparum. Downloaded from http://www.geneontology.org/

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See: QuickStart